You could say that about Madlax as well.
A browse of TV Tropes on my phone got me the following on
Madlax. The
Bi the Way trope for Madlax herself via her attempt to date that guy in Episode 1. Then her cuddle with Vanessa who she refers to as "Her Princess." Finally for her eventual ship with Limelda at the end. I have no memory of the "Her Princess" line.
They also list the
Just Friends "... Yeah right" trope for Madlax/Vanessa and Vanessa/Elenore.
Finally they once again have
Psycho Lesbian for Limelda and her obsession with Madlax. You have to wonder why Aya Hisakawa got two roles of that nature.
From what I have read about token yuri in anime I'm reasonably certain the implied yuri in GwG is deliberate. When you add in some of the stuff from Cazzy and .hack I am sure they intentionally use their stories to make commentary on human relationships, and in particular they focus on relationships between women in a variety of contexts. I think the dividing line between good and bad relationships for BeeTrain is healthy vs unhealthy as opposed to gender or sex.
Edit: Added the links now that I am on an actual computer.
Also found a few other bits.
Elenore got listed as
Badass Lesbian.And for the local Elenore fangirl TV Tropes named her Greater Goddess of
Ninja Maids.Vanessa got
Bodyguard Crush for her realtionship with Madlax; which as it happens they read as mutual. And
Lipstick Lesbian. They claim they deified her for this, but I can't find the reference on their deity page. Finally she also got
Ship Tease.